2VUR: O-glcnacase nagj

Chemical dissection of the link between Streptozotocin, O-GlcNAc and pancreatic cell death. Determined by X-ray diffraction at 2.2 Å resolution. Released 10 Feb 2009.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: CLOSTRIDIUM PERFRINGENS
Chains: 2
Atoms: 9,809
Mol. weight: 134.01 kDa
Ligands: YX1
Released: 10 Feb 2009

Explore 2VUR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2VUR contains 69 α-helices and 48 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 35 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	42-45	4
α-helix	49-50	2
β-strand	52-55	4	1
β-strand	60-61	2	2
α-helix	62-63	2
β-strand	65-69	5	1
α-helix	76-88	13
β-strand	92-93	2	1
α-helix	94	1
β-strand	102-108	7	1
α-helix	114-120	7
β-strand	133-138	6	1
β-strand	141-146	6	1
α-helix	149-162	14
β-strand	164	1	2
β-strand	167-168	2	2
β-strand	171-175	5	1
β-strand	181-185	5	3
α-helix	192-194	3
α-helix	195-207	13
β-strand	212-215	4	3
α-helix	221-223	3
α-helix	230-232	3
α-helix	233-248	16
β-strand	252-257	6	3
α-helix	259-261	3
α-helix	267-285	19
β-strand	291-295	5	3
α-helix	304-314	11
α-helix	315-320	6
α-helix	321-322	2
α-helix	325-328	4
β-strand	329-331	3	3
α-helix	337-340	4
β-strand	341-342	2	4
β-strand	345-346	2	4
α-helix	348-356	9
β-strand	362-365	4	3
β-strand	375	1	5
α-helix	377-387	11
α-helix	390	1
β-strand	391-395	5	3
β-strand	415	1	5
α-helix	419-421	3
β-strand	423-428	6	3
α-helix	437-449	13
α-helix	456-468	13
α-helix	469-471	3
α-helix	472-479	8
β-strand	485-486	2	6
β-strand	492-493	2	6
α-helix	496	1
α-helix	499-513	15
α-helix	519-542	24
α-helix	545-576	32
α-helix	580-599	20
α-helix	606-610	5
α-helix	611-617	7
α-helix	621-623	3

Chain B: 34 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	42-45	4
α-helix	49-50	2
β-strand	52-55	4	7
β-strand	60-61	2	8
α-helix	62-63	2
β-strand	65-69	5	7
α-helix	76-88	13
β-strand	92-93	2	7
β-strand	102-108	7	7
α-helix	114-120	7
β-strand	133-138	6	7
β-strand	141-146	6	7
α-helix	149-162	14
β-strand	164	1	8
β-strand	167-168	2	8
β-strand	171-175	5	7
β-strand	181-185	5	9
α-helix	192-194	3
α-helix	195-207	13
β-strand	212-215	4	9
α-helix	221-223	3
α-helix	230-232	3
α-helix	233-235	3
α-helix	236-248	13
β-strand	252-257	6	9
α-helix	259-261	3
α-helix	267-286	20
β-strand	291-295	5	9
α-helix	304-314	11
α-helix	315-320	6
α-helix	321-322	2
α-helix	326-328	3
β-strand	329-331	3	9
α-helix	337-340	4
β-strand	341-342	2	10
β-strand	345-346	2	10
α-helix	348-356	9
β-strand	362-365	4	9
β-strand	375	1	11
α-helix	377-386	10
β-strand	391-395	5	9
β-strand	415	1	11
α-helix	419-421	3
β-strand	423-428	6	9
α-helix	437-449	13
α-helix	456-468	13
α-helix	469-471	3
α-helix	472-479	8
β-strand	485-486	2	12
β-strand	492-493	2	12
α-helix	495-496	2
α-helix	499-513	15
α-helix	519-542	24
α-helix	545-576	32
α-helix	580-599	20
α-helix	606-610	5
α-helix	611-617	7
α-helix	621-623	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
O-glcnacase nagj	A, B	protein	594	CLOSTRIDIUM PERFRINGENS	Q0TR53 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2VUR_1 O-GLCNACASE NAGJ (chains A, B)
VGPKTGEENQVLVPNLNPTPENLEVVGDGFKITSSINLVGEEEADENAVNALREFLTANN
IEINSENDPNSTTLIIGEVDDDIPELDEALNGTTAENLKEEGYALVSNDGKIAIEGKDGD
GTFYGVQTFKQLVKESNIPEVNITDYPTVSARGIVEGFYGTPWTHQDRLDQIKFYGENKL
NTYIYAPKDDPYHREKWREPYPESEMQRMQELINASAENKVDFVFGISPGIDIRFDGDAG
EEDFNHLITKAESLYDMGVRSFAIYWDDIQDKSAAKHAQVLNRFNEEFVKAKGDVKPLIT
VPTEYDTGAMVSNGQPRAYTRIFAETVDPSIEVMWTGPGVVTNEIPLSDAQLISGIYNRN
MAVWWNYPVTDYFKGKLALGPMHGLDKGLNQYVDFFTVNPMEHAELSKISIHTAADYSWN
MDNYDYDKAWNRAIDMLYGDLAEDMKVFANHSTRMDNKTWAKSGREDAPELRAKMDELWN
KLSSKEDASALIEELYGEFARMEEACNNLKANLPEVALEECSRQLDELITLAQGDKASLD
MIVAQLNEDTEAYESAKEIAQNKLNTALSSFAVISEKVAQSFIQEALSFDLTLI

Ligands and cofactors

ID	Name	Formula	Copies
YX1	2-deoxy-2-{[(2-hydroxy-1-methylhydrazino)carbonyl]amino}-beta-D-glucopyranose	C8 H17 N3 O7	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Chemical Dissection of the Link between Streptozotocin, O-Glcnac, and Pancreatic Cell Death. Pathak, S., Dorfmueller, H.C., Borodkin, V.S. et al. Chem Biol (2008) 15:799. DOI 10.1016/J.CHEMBIOL.2008.06.010 · PubMed

Other PDB entries of the same protein (UniProt Q0TR53 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2J1A 1.49 Å, Structure of CBM32 from Clostridium perfringens beta-N- acetylhexosaminidase GH84C in…
2OZN 1.6 Å, The Cohesin-Dockerin Complex of NagJ and NagH from Clostridium perfringens
2W1N 1.8 Å, cohesin and fibronectin type-III double module construct from the Clostridium…
2V5C 2.1 Å, Family 84 glycoside hydrolase from Clostridium perfringens, 2.1 Angstrom structure
2CBI 2.25 Å, Structure of the Clostridium perfringens NagJ family 84 glycoside hydrolase, a homologue…
2X0Y 2.25 Å, Screening-based discovery of drug-like O-GlcNAcase inhibitor scaffolds
2J62 2.26 Å, Structure of a bacterial O-glcnacase in complex with glcnacstatin
2J7M 2.3 Å, Characterization of a Family 32 CBM
7KHV 2.3 Å, Cpoga in complex with ligand 54
2WB5 2.31 Å, GlcNAcstatins are nanomolar inhibitors of human O-GlcNAcase inducing cellular…
2CBJ 2.35 Å, Structure of the Clostridium perfringens NagJ family 84 glycoside hydrolase, a homologue…
2J1E 2.4 Å, High Resolution Crystal Structure of CBM32 from a N-acetyl-beta- hexosaminidase in…

Browse structure collections

About this viewer

MolViewer shows 2VUR directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.